4ESJ

RESTRICTION ENDONUCLEASE DpnI IN COMPLEX WITH TARGET DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.199 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Crystal structure and mechanism of action of the N6-methyladenine-dependent type IIM restriction endonuclease R.DpnI.

Siwek, W.Czapinska, H.Bochtler, M.Bujnicki, J.M.Skowronek, K.

(2012) Nucleic Acids Res 40: 7563-7572

  • DOI: https://doi.org/10.1093/nar/gks428
  • Primary Citation of Related Structures:  
    4ESJ

  • PubMed Abstract: 

    DNA methylation-dependent restriction enzymes have many applications in genetic engineering and in the analysis of the epigenetic state of eukaryotic genomes. Nevertheless, high-resolution structures have not yet been reported, and therefore mechanisms of DNA methylation-dependent cleavage are not understood. Here, we present a biochemical analysis and high-resolution DNA co-crystal structure of the N(6)-methyladenine (m6A)-dependent restriction enzyme R.DpnI. Our data show that R.DpnI consists of an N-terminal catalytic PD-(D/E)XK domain and a C-terminal winged helix (wH) domain. Surprisingly, both domains bind DNA in a sequence- and methylation-sensitive manner. The crystal contains R.DpnI with fully methylated target DNA bound to the wH domain, but distant from the catalytic domain. Independent readout of DNA sequence and methylation by the two domains might contribute to R.DpnI specificity or could help the monomeric enzyme to cut the second strand after introducing a nick.


  • Organizational Affiliation

    Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, Trojdena 4, 02-109 Warsaw, Poland.


Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Type-2 restriction enzyme DpnI
A, B
257Streptococcus pneumoniae TIGR4Mutation(s): 1 
Gene Names: dpnCspr1665
EC: 3.1.21.4
UniProt
Find proteins for P0A460 (Streptococcus pneumoniae (strain ATCC BAA-255 / R6))
Explore P0A460 
Go to UniProtKB:  P0A460
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A460
Sequence Annotations
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  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (5'-D(*CP*TP*GP*GP*(6MA)P*TP*CP*CP*AP*G)-3')
C, D, E, F
10synthetic construct
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download Ideal Coordinates CCD File 
L [auth D]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
G [auth A],
H [auth A],
J [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
AZI
Query on AZI

Download Ideal Coordinates CCD File 
I [auth A]AZIDE ION
N3
IVRMZWNICZWHMI-UHFFFAOYSA-N
UNX
Query on UNX

Download Ideal Coordinates CCD File 
K [auth C],
M [auth D]
UNKNOWN ATOM OR ION
X
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.199 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 130.518α = 90
b = 98.411β = 112.21
c = 83.884γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
SHELXDEphasing
DMmodel building
ARP/wARPmodel building
REFMACrefinement
CNSrefinement
XDSdata reduction
SCALAdata scaling
DMphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-06-13
    Type: Initial release
  • Version 1.1: 2012-10-17
    Changes: Database references
  • Version 1.2: 2024-02-28
    Changes: Data collection, Database references, Derived calculations